Advances and challenges in metatranscriptomic analysis
Sequencing-based analyses of microbiomes have traditionally focused on addressing the
question of community membership and profiling taxonomic abundance through amplicon …
question of community membership and profiling taxonomic abundance through amplicon …
Metagenomics, metatranscriptomics, and metabolomics approaches for microbiome analysis: supplementary issue: bioinformatics methods and applications for big …
V Aguiar-Pulido, W Huang… - Evolutionary …, 2016 - journals.sagepub.com
Microbiomes are ubiquitous and are found in the ocean, the soil, and in/on other living
organisms. Changes in the microbiome can impact the health of the environmental niche in …
organisms. Changes in the microbiome can impact the health of the environmental niche in …
[HTML][HTML] Current concepts, advances, and challenges in deciphering the human microbiota with metatranscriptomics
T Ojala, AE Häkkinen, E Kankuri, M Kankainen - Trends in Genetics, 2023 - cell.com
Metatranscriptomics refers to the analysis of the collective microbial transcriptome of a
sample. Its increased utilization for the characterization of human-associated microbial …
sample. Its increased utilization for the characterization of human-associated microbial …
Metatranscriptomics for the human microbiome and microbial community functional profiling
Shotgun metatranscriptomics (MTX) is an increasingly practical way to survey microbial
community gene function and regulation at scale. This review begins by summarizing the …
community gene function and regulation at scale. This review begins by summarizing the …
SAMSA2: a standalone metatranscriptome analysis pipeline
Background Complex microbial communities are an area of growing interest in biology.
Metatranscriptomics allows researchers to quantify microbial gene expression in an …
Metatranscriptomics allows researchers to quantify microbial gene expression in an …
IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and
often result in sub-optimal data usage. Here we present IMP, a reproducible and modular …
often result in sub-optimal data usage. Here we present IMP, a reproducible and modular …
Systematic profiling of the chicken gut microbiome reveals dietary supplementation with antibiotics alters expression of multiple microbial pathways with minimal …
A Zou, K Nadeau, X Xiong, PW Wang, JK Copeland… - Microbiome, 2022 - Springer
Background The emergence of antimicrobial resistance is a major threat to global health
and has placed pressure on the livestock industry to eliminate the use of antibiotic growth …
and has placed pressure on the livestock industry to eliminate the use of antibiotic growth …
A deep learning approach reveals unexplored landscape of viral expression in cancer
About 15% of human cancer cases are attributed to viral infections. To date, virus expression
in tumor tissues has been mostly studied by aligning tumor RNA sequencing reads to …
in tumor tissues has been mostly studied by aligning tumor RNA sequencing reads to …
Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality
Y Jiang, X Xiong, J Danska, J Parkinson - Microbiome, 2016 - Springer
Background Metatranscriptomics is emerging as a powerful technology for the functional
characterization of complex microbial communities (microbiomes). Use of unbiased RNA …
characterization of complex microbial communities (microbiomes). Use of unbiased RNA …
Microbial bioinformatics for food safety and production
In the production of fermented foods, microbes play an important role. Optimization of
fermentation processes or starter culture production traditionally was a trial-and-error …
fermentation processes or starter culture production traditionally was a trial-and-error …